syndiva: syndiva.py annotate

annotate syndiva.py @ 0:0254731f047b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c

author	iuc
date	Thu, 23 Jun 2022 22:32:13 +0000
parents
children

rev	line source
0 0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	1 #!/usr/bin/env python
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	2 # title : syndiva.py
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	3 # description : This script will analyze fasta files, look for restriction sites,
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	4 # cut the sequences around the restriction sites,
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	5 # translate the nucleic sequences into amino acids sequences.
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	6 # author : Fabienne Wong Jun Tai and Benjamin Dartigues
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	7 # creation date : 20121107
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	8 # version : 1.0 - revised November 2012
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	9 # version : 1.1 - revised March 2022
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	10 # usage : python syndiva.py -i file.fasta -o /output/dir/ -p pattern -5 seq_restric_5'-3 seq_restric_3'
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	11 # notes :
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	12 # # python_version :3.7.11
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	13 # # biopython_max_version :1.72
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	14 # ==============================================================================
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	15 import math
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	16 import re
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	17 import subprocess
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	18 import sys
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	19
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	20 import matplotlib
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	21 import numpy
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	22 from args import Args
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	23 from args import get_os_path_join, get_os_path_name
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	24 from Bio import pairwise2
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	25 from Bio import SeqIO
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	26 from Bio.Seq import Seq
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	27 from Bio.Seq import translate
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	28 from Bio.SubsMat import MatrixInfo
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	29
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	30 matplotlib.use('Agg')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	31 from matplotlib import pyplot as plot # noqa: I202,E402
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	32
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	33
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	34 args = Args()
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	35 # Variables initialization
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	36 directory = args.output_dir
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	37 mcl_file = get_os_path_join(directory, "mcl.in")
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	38 mcl_output = get_os_path_join(directory, "mcl.out")
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	39 html_file = get_os_path_join(directory, "syndiva_report.html")
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	40 graph_pic = get_os_path_join(directory, "distri.png")
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	41 input_file = get_os_path_name(args.input)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	42 site_res_5 = args.site_res_5
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	43 site_res_3 = args.site_res_3
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	44 tag = {'mut': [], 'ok_stop_ext': [], 'stop': [], 'no_restric': [], 'no_multiple': [], 'amber': []}
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	45 all_seq = []
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	46 all_seq_fasta = {} # dictionnary that will store information about all the sequences
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	47 good_seq = {} # dictionnary that will store information about the valid sequences
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	48 identical_clones = {}
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	49 var_seq_common = {} # dictionnary that will store the number of sequences that share the same variable parts
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	50 align_scores = []
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	51 nb_var_part = 0
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	52
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	53
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	54 def get_identity(str1, str2):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	55 if len(str2) > len(str1):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	56 return (len(str2) - len([i for i in range(len(str1)) if str1[i] != str2[i]])) / len(str2)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	57 else:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	58 return (len(str1) - len([i for i in range(len(str1)) if str1[i] != str2[i]])) / len(str1)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	59
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	60
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	61 def reverse_complement(_seq):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	62 return str(Seq(_seq).reverse_complement())
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	63
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	64
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	65 def generate_aln(seq_dic, ids): # sourcery skip: use-join
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	66 # Multiple Sequence Alignment via ClustalO
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	67 _input = ''
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	68 for sequence_id in ids:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	69 _input += '>%s\n%s\n' % (sequence_id, re.sub("(.{80})", "\\1\n", seq_dic[sequence_id]['prot'], re.DOTALL))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	70 p = subprocess.Popen(["clustalo", "-i", "-", "--outfmt", "clu"], shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE, stdin=subprocess.PIPE, universal_newlines=True)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	71 aln_out, aln_err = p.communicate(input=_input)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	72 return aln_out
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	73
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	74
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	75 def report_html(_html_file, _tag, _all_seq, _good_seq, _all_seq_fasta, _identical_clones, _nb_var_part, _var_seq_common, _align_scores, _args):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	76 # Generate the html file for the report
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	77 _all_seq.sort()
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	78 for key in _tag.keys():
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	79 _tag[key].sort()
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	80 _good_seq = dict(sorted(_good_seq.items()))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	81 good_ids = _good_seq.keys()
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	82 w = open(_html_file, 'w')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	83 w.write(
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	84 '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN""http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	85 'lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /><title>SynDivA Report</title><link '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	86 'href="http://twitter.github.com/bootstrap/assets/css/bootstrap.css" rel="stylesheet" /><style type="text/css">body {padding-top: 40px;}.subhead {padding: 40px '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	87 '0;}.subhead h1 {font-size: 60px;}.fasta { font-family: Monaco, Menlo, Consolas, "Courier New", monospace; font-size: 12px;}code.grey{color: '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	88 '#636D71;}</style></head><body><a id="top"></a><div class="navbar navbar-fixed-top"><div class="navbar-inner"><div class="container"><a class="brand" href="#top">SynDivA '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	89 'Report</a><div class="nav-collapse collapse"><ul class="nav"><li><a href="#input">Input data</a></li><li><a href="#analysis">Sequences analysis</a></li><li><a '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	90 'href="#variable">Variable regions analysis</a></li><li><a href="#cluster">Clustering</a></li><li><a href="#stat">Statistics</a></li><li><a '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	91 'href="#annex">Annex</a></li></ul></div></div></div></div><div class="container-fluid"><header class="subhead"><h1>SynDivA Report</h1></header><div '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	92 'class="page-header"><a id="input"></a><h2>Input data</h2></div>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	93
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	94 # Input data
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	95 w.write(
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	96 '<p>Input file:<br/><code class="grey">%s</code></p><p>Number of sequences in input file:<br/><code class="grey">%d</code></p><p>Pattern of the sequence bank:<br/><code '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	97 'class="grey">%s</code></p><p>5\' restriction site:<br/><code class="grey">%s</code></p><p>3\' restriction site:<br/><code class="grey">%s</code></p>' % (
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	98 input_file, len(_all_seq), _args.pattern, _args.site_res_5, _args.site_res_3))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	99
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	100 # Sequence analysis
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	101 w.write(
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	102 '<div class="page-header"><a id="analysis"></a><h2>Sequences analysis</h2></div><p>Caption:</p><ul><li class="text-success">Valid sequences that will be part of the next '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	103 'analysis </li><li class="text-warning">Good sequences but will not be part of the next analysis</li><li class="text-error">Rejected sequences</li></ul><table '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	104 'class="table table-striped table-bordered"><tr><th class="text-error">Absence of restriction sites</th><th class="text-error">Incorrect number of nucleotides between '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	105 'the restriction sites</th><th class="text-error">Stop codon <u>inside</u> the area of interest</th><th class="text-warning">Mutation in the conserved regions</th><th '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	106 'class="text-success">Valid sequences</th><th>Amber codon in the sequence (<u>inside</u> the area of interest)</th></tr>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	107 w.write(
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	108 '<tr><td class="text-error">%d sequence(s) (%.2f%%)</td><td class="text-error">%d sequence(s) (%.2f%%)</td><td class="text-error">%d sequence(s) (%.2f%%)</td><td '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	109 'class="text-warning">%d sequence(s) (%.2f%%)</td><td class="text-success">%d sequence(s) (%.2f%%)</td><td>%d sequence(s)</td></tr>' % (
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	110 len(_tag['no_restric']), float(len(_tag['no_restric'])) / float(len(_all_seq)) * 100, len(_tag['no_multiple']), float(len(_tag['no_multiple'])) / float(len(_all_seq)) * 100, len(_tag['stop']),
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	111 float(len(_tag['stop'])) / float(len(_all_seq)) * 100, len(_tag['mut']), float(len(_tag['mut'])) / float(len(_all_seq)) * 100, len(good_ids),
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	112 float(len(good_ids)) / float(len(_all_seq)) * 100,
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	113 len(_tag['amber'])))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	114 w.write(
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	115 '<tr><td class="text-error">%s</td><td class="text-error">%s</td><td class="text-error">%s</td><td class="text-warning">%s</td><td '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	116 'class="text-success">%s</td><td>%s</td></tr></table>' % (
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	117 '<br/>'.join(_tag['no_restric']), '<br/>'.join(_tag['no_multiple']), '<br/>'.join(_tag['stop']), '<br/>'.join(_tag['mut']), '<br/>'.join(good_ids), '<br/>'.join(_tag['amber'])))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	118 # Variable regions analysis
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	119 w.write(
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	120 '<div class="page-header"><a id="variable"></a><h2>Variable regions analysis</h2></div><p>The following group of sequences are identical clones on the variable '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	121 'regions:</p>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	122 identical_clones_seq = _identical_clones.keys()
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	123 if identical_clones_seq:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	124 for seq in identical_clones_seq:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	125 ids = list(set(_identical_clones[seq])) # return only one occurrence of each item in the list
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	126 w.write('<div class="row-fluid"><div class="span5"><pre>%d sequences (%.2f%% of valid sequences)<br/>%s</pre></div>' % (
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	127 len(ids), float(len(ids)) / float(len(good_ids)) * 100, '<br/>'.join(ids)))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	128 w.write('<div class="span3"><table class="table table-striped table-bordered"><thead><tr><th>Variable region</th><th>Repeated sequence</th></tr></thead><tbody>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	129 for z in range(len(_good_seq[ids[0]]['var'])):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	130 w.write('<td>%d</td><td>%s</td></tr>' % (z + 1, _good_seq[ids[0]]['var'][z]))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	131 w.write('</tbody></table></div></div>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	132 else:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	133 w.write('<p>No clone was found.</p>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	134
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	135 first = True
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	136 for i in range(_nb_var_part):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	137 keys = []
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	138 for k in _var_seq_common[str(i + 1)].keys():
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	139 nb = _var_seq_common[str(i + 1)][k]
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	140 if nb > 1:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	141 if first:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	142 w.write(
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	143 '<p>Here\'s the distribution of the repeated sequences in variable regions:</p><table class="table table-striped table-bordered"><thead><tr><th>Variable '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	144 'region</th><th>Repeated sequence</th><th>Number of occurrences (percentage of valid sequences)</th></tr></thead><tbody>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	145 first = False
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	146 keys.append(k)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	147 else:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	148 keys.append(k)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	149 nb = len(keys)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	150 if nb != 0:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	151 w.write('<tr>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	152 for z in range(nb):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	153 if z == 0:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	154 w.write('<td rowspan="%d">%d</td>' % (nb, i + 1))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	155 w.write('<td>%s</td><td>%d (%.2f%%)</td></tr>' % (
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	156 keys[z], _var_seq_common[str(i + 1)][keys[z]], float(_var_seq_common[str(i + 1)][keys[z]]) / float(len(good_ids)) * 100))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	157 w.write('</tbody></table>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	158 # Clustering
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	159 w.write('<div class="page-header"><a id="cluster"></a><h2>Clustering</h2></div><p>The following clusters were generated by MCL:</p>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	160 for line in open(mcl_output, 'r'):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	161 w.write('<div class="row-fluid"><div class="span6"><pre>%d sequences (%.2f%% of valid sequences)<br/>%s</pre></div></div>' % (
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	162 len(line.split("\t")), float(len(line.split("\t"))) / float(len(good_ids)) * 100, '<br/>'.join(line.split("\t"))))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	163 # Statistics
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	164 w.write('<div class="page-header"><a id="stat"></a><h2>Statistics</h2></div>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	165 w.write('<p>Here\'s some statistics about the valid sequences:</p><p>Mean for the pairwise alignement scores: %.2f<br/>Standard deviation: %.2f</p>' % (
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	166 float(numpy.mean(_align_scores)), float(numpy.std(_align_scores))))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	167 w.write('<div class="row-fluid"><div class="span6"><img src="%s" alt="Distribution of the pairwise alignment score"></div>' % get_os_path_name(graph_pic))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	168 w.write('<div class="span6"><table class="table table-striped table-bordered"><thead><tr><th>Pairwise Alignment Score</th><th>Number of occurrences</th></tr></thead><tbody>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	169 uniq_scores = sorted(list(set(_align_scores)))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	170 scores_dic = {}
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	171 for _score in uniq_scores:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	172 scores_dic[_score] = _align_scores.count(_score)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	173 scores_dic = dict(sorted(scores_dic.items()))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	174 scores = scores_dic.items()
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	175 # scores.sort()
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	176 for el in scores:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	177 w.write('<tr><td>%.2f</td><td>%d</td></tr>' % (el[0], el[1]))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	178 w.write('</tbody></table></div></div>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	179 # Annex
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	180 w.write('<div class="page-header"><a id="annex"></a><h2>Annex</h2></div>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	181 w.write('<p><strong>Valid protein sequences</strong> in FASTA format:</p><textarea class="span8 fasta" type="text" rows="20" readonly="readonly">')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	182 for _id in good_ids:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	183 w.write('>%s\n%s\n' % (_id, re.sub("(.{80})", "\\1\n", _good_seq[_id]['prot'], re.DOTALL)))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	184 w.write('</textarea>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	185 aln_out = generate_aln(_good_seq, good_ids)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	186 w.write(
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	187 '<p>Multiple sequence alignment of the <strong>valid sequences</strong> generated by Clustal Omega:</p><textarea class="span8 fasta" type="text" rows="20" '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	188 'readonly="readonly">%s</textarea>' % str(
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	189 aln_out))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	190
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	191 if _tag['no_multiple']:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	192 w.write(
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	193 '<p><strong>Protein sequences with an incorrect number of nucleotides between the restriction sites</strong> in FASTA format:</p><textarea class="span8 fasta" '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	194 'type="text" rows="20" readonly="readonly">')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	195 for _id in _tag['no_multiple']:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	196 w.write('>%s\n%s\n' % (_id, re.sub("(.{80})", "\\1\n", _all_seq_fasta[_id]['prot'], re.DOTALL)))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	197 w.write('</textarea>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	198
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	199 if _tag['mut']:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	200 w.write('<p><strong>Mutated protein sequences</strong> in FASTA format:</p><textarea class="span8 fasta" type="text" rows="20" readonly="readonly">')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	201 for _id in _tag['mut']:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	202 w.write('>%s\n%s\n' % (_id, re.sub("(.{80})", "\\1\n", _all_seq_fasta[_id]['prot'], re.DOTALL)))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	203 w.write('</textarea>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	204 aln_out = generate_aln(_all_seq_fasta, _tag['mut'])
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	205
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	206 w.write(
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	207 '<p>Multiple sequence alignment of the <strong>mutated sequences</strong> generated by Clustal Omega:</p><textarea class="span8 fasta" type="text" rows="20" '
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	208 'readonly="readonly">%s</textarea>' % str(
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	209 aln_out))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	210
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	211 if _tag['stop']:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	212 w.write('<p><strong>Protein sequences with a stop codon</strong> in FASTA format:</p><textarea class="span8 fasta" type="text" rows="20" readonly="readonly">')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	213 for _id in _tag['stop']:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	214 w.write('>%s\n%s\n' % (_id, re.sub("(.{80})", "\\1\n", _all_seq_fasta[_id]['prot'], re.DOTALL)))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	215 w.write('</textarea>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	216
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	217 if _tag['amber']:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	218 w.write('<p><strong>Protein sequences with an amber codon</strong> in FASTA format:</p><textarea class="span8 fasta" type="text" rows="20" readonly="readonly">')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	219 for _id in _tag['amber']:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	220 w.write('>%s\n%s\n' % (_id, re.sub("(.{80})", "\\1\n", _all_seq_fasta[_id]['prot'], re.DOTALL)))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	221 w.write('</textarea>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	222
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	223 w.write('</div></body></html>')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	224 w.close()
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	225
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	226
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	227 nb_seq = len(list(SeqIO.parse(args.input, "fasta")))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	228
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	229 for seq_record in SeqIO.parse(args.input, "fasta"):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	230 seq_id = seq_record.id
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	231 seq = str(seq_record.seq)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	232 seq = seq.upper()
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	233 all_seq.append(seq_id)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	234 # Checking if both restriction sites are present in the sequence
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	235 if site_res_5 in seq and site_res_3 in seq:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	236 valid = True
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	237 else:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	238 valid = False
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	239 tag['no_restric'].append(seq_id)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	240 # If sequence has both restriction sites, checking if it is necessary to take the reverse complement strand
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	241 if valid:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	242 site_res_5_pos = seq.index(site_res_5)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	243 site_res_3_pos = seq.index(site_res_3)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	244 # If site_res_5_pos > site_res_3_pos, reverse complement strand has to be calculated
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	245 if site_res_5_pos > site_res_3_pos:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	246 # Checking if the number of nucleic acids between the restriction sites is a multiple of 3
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	247 length = math.fabs((site_res_5_pos + len(site_res_5)) - site_res_3_pos)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	248 valid = length % 3 == 0
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	249 cut_seq = seq[:site_res_5_pos + len(site_res_5)]
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	250 cut_seq = reverse_complement(cut_seq)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	251
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	252 # Else if site_res_5_pos < site_res_3_pos, use the sequence as it is
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	253 else:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	254 # Checking if the number of nucleic acids between the restriction sites is a multiple of 3
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	255 length = math.fabs((site_res_3_pos + len(site_res_3)) - site_res_5_pos)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	256 valid = length % 3 == 0
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	257 cut_seq = seq[site_res_5_pos:]
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	258 # If the number of nucleic acids between the restriction sites isn't a multiple of 3, put the sequence away
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	259 if not valid:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	260 tag['no_multiple'].append(seq_id)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	261 prot_seq = translate(cut_seq)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	262 all_seq_fasta[seq_id] = {}
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	263 all_seq_fasta[seq_id]['prot'] = prot_seq
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	264 else:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	265 # Translate nucleic sequence into amino acid sequence
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	266 prot_seq = translate(cut_seq)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	267 all_seq_fasta[seq_id] = {}
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	268 all_seq_fasta[seq_id]['prot'] = prot_seq
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	269
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	270 # Looking for stop codon in the sequence and getting their position in the sequence
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	271 if '*' in prot_seq:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	272 pos_stop = [m.start() for m in re.finditer(r"\*", prot_seq)]
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	273 stop = False
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	274 # Checking if stop codon is between the restriction sites, also checking if it is an amber codon. if stop codon other than amber codon -> tag stop
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	275 for i in range(len(pos_stop)):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	276 if pos_stop[i] < length / 3:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	277 stop_codon_nuc = cut_seq[pos_stop[i] * 3:pos_stop[i] * 3 + 3]
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	278 if stop_codon_nuc != "TAG":
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	279 tag['stop'].append(seq_id)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	280 stop = True
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	281 break
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	282 else:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	283 if seq_id not in tag['amber']:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	284 tag['amber'].append(seq_id)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	285 # If stop codon wasn't found between the restriction sites
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	286 if not stop:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	287 """
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	288 # Checking if there is a stop codon outside the restriction sites. If yes -> tag ok_stop_ext
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	289 for i in range(len(pos_stop)):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	290 if (pos_stop[i] > length/3):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	291 stop_codon_nuc = cut_seq[pos_stop[i]3:pos_stop[i]3+3]
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	292 if stop_codon_nuc != "TAG":
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	293 tag['ok_stop_ext'].append(seq_id)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	294 stop = True
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	295 break
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	296 else:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	297 if (seq_id not in tag['amber']):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	298 tag['amber'].append(seq_id)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	299 """
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	300 # Checking if there was a mutation in the fix part, if yes -> tag mut else retrieve variable parts
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	301 mut = False
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	302 pattern_part = args.pattern.split(":")
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	303 tmp_prot_seq = prot_seq
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	304 var_parts = []
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	305 for i in range(len(pattern_part) - 1): # not checking the latest fix part
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	306 part = pattern_part[i]
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	307 # If part is fix
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	308 if not part[0].isdigit():
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	309 # If part not in prot_seq -> mutation, flag then break
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	310 if part not in tmp_prot_seq:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	311 mut = True
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	312 tag['mut'].append(seq_id)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	313 break
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	314 # Else, store the variable part if exist then remove the fix part + variable part (tmp_prot_seq starts at the end of part)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	315 else:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	316 pos_fix = tmp_prot_seq.index(part)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	317 if pos_fix != 0:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	318 var_parts.append(tmp_prot_seq[0:pos_fix])
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	319 tmp_prot_seq = tmp_prot_seq[pos_fix + len(part):]
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	320 # Else part is variable
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	321 else:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	322 nb_var_part += 1
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	323 # Treating latest fix part if no mutation before
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	324 if not mut:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	325 last_part = pattern_part[-1]
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	326 last_var = pattern_part[-2]
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	327 if '-' in last_var:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	328 var_max = int(last_var.split('-')[1])
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	329 else:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	330 var_max = int(last_var)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	331 last_part = last_part[0:var_max + 1]
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	332 if last_part not in tmp_prot_seq:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	333 mut = True
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	334 tag['mut'].append(seq_id)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	335 else:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	336 pos_fix = tmp_prot_seq.index(last_part)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	337 if pos_fix != 0:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	338 var_parts.append(tmp_prot_seq[0:pos_fix])
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	339 # If no mutation the sequence is validated and all the info are stored
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	340 if not mut:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	341 good_seq[seq_id] = {}
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	342 good_seq[seq_id]['dna'] = cut_seq
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	343 good_seq[seq_id]['prot'] = prot_seq
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	344 good_seq[seq_id]['var'] = var_parts
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	345
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	346 # If all sequences are invalid, the program will exit as there is no data to continue
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	347 if not good_seq:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	348 sys.exit("There is only one valid sequence among the input data. At least 2 valid sequences are necessary to proceed to the next step. The program will now exit")
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	349 elif len(good_seq.keys()) == 1:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	350
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	351 sys.exit("There is only one valid sequence among the input data. At least 2 valid sequences are necessary to proceed to the next step. The program will now exit")
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	352
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	353 # Initialization of dict var_seq_common
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	354 for n in range(nb_var_part):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	355 var_seq_common[str(n + 1)] = {}
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	356
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	357 # Opening the file where the mcl input will be written
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	358 with open(mcl_file, 'w+') as mcl:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	359 seq_keys = good_seq.keys()
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	360 for i in range(len(seq_keys)):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	361 var_1 = good_seq[list(seq_keys)[i]]['var']
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	362
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	363 # Classifying variable sequences
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	364 for k in range(len(var_1)):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	365 try:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	366 var_seq_common[str(k + 1)][var_1[k]] += 1
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	367 except KeyError:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	368 var_seq_common[str(k + 1)][var_1[k]] = 1
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	369
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	370 for j in range(i + 1, len(seq_keys)):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	371 var_2 = good_seq[list(seq_keys)[j]]['var']
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	372 score = 0.0
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	373 # Comparing the sequences' variable parts to find identical clones
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	374 if var_1 == var_2:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	375 try:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	376 clone_seq = "".join(var_1)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	377 identical_clones[clone_seq].extend([seq_keys[i], seq_keys[j]])
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	378 except KeyError:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	379 identical_clones[clone_seq] = [seq_keys[i], seq_keys[j]]
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	380 # Align the 2 sequences using NWalign_PAM30 => replace by pairwise2
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	381 seq_1 = ''.join(var_1)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	382 seq_2 = ''.join(var_2)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	383 matrix = MatrixInfo.pam30
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	384 if len(seq_2) > len(seq_1):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	385 score = get_identity(pairwise2.align.globalds(seq_1, seq_2, matrix, -11, -1)[0][0], pairwise2.align.globalds(seq_1, seq_2, matrix, -11, -1)[0][1]) * 100
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	386 else:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	387 score = get_identity(pairwise2.align.globalds(seq_2, seq_1, matrix, -11, -1)[0][0], pairwise2.align.globalds(seq_2, seq_1, matrix, -11, -1)[0][1]) * 100
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	388 align_scores.append(score)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	389 mcl.write('%s\t%s\t%0.2f\n' % (list(seq_keys)[i], list(seq_keys)[j], score))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	390
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	391 # Clusters formation
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	392 subprocess.call(["mcl", mcl_file, "--abc", "-I", "6.0", "-o", mcl_output], shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	393
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	394 # Producing distribution graph
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	395 plot.hist(align_scores, bins=numpy.arange(0, 101, 2))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	396 plot.xlabel('Pairwise Alignment Score')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	397 plot.ylabel('Number of occurrences')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	398 plot.title('Distribution of the pairwise alignment score')
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	399 plot.grid(True)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	400 plot.savefig(graph_pic)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	401
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	402 # Generating html report
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	403 report_html(html_file, tag, all_seq, good_seq, all_seq_fasta, identical_clones, nb_var_part, var_seq_common, align_scores, args)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	404
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	405 # Removing intermediate files
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	406 subprocess.call(["rm", mcl_file, mcl_output], shell=False)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c iuc parents: diff changeset	407 print("HTML report has been generated in the output directory. The program will now exit.")

Mercurial > repos > iuc > syndiva

annotate syndiva.py @ 0:0254731f047b draft default tip